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## ----setup, include=FALSE-----------------------------------------------------
library(nodeSub)
library(ggplot2)
knitr::opts_chunk$set(echo = TRUE)
plot_phyDat <- function(phyDat_alignment) {
vx <- as.data.frame(phyDat_alignment)
num_entries <- nrow(vx) * ncol(vx)
to_plot <- matrix(nrow = num_entries, ncol = 3)
cnt <- 1
for (i in 1:nrow(vx)) {
for (j in 1:ncol(vx)) {
to_plot[cnt, ] <- c(i, j, vx[i, j])
cnt <- cnt + 1
}
}
colnames(to_plot) <- c("x", "y", "base")
to_plot <- tibble::as_tibble(to_plot)
to_plot$x <- as.numeric(to_plot$x)
to_plot$y <- as.numeric(to_plot$y)
ggplot(to_plot, aes(x = x, y = y, fill = base)) +
geom_tile()
}
## ----start--------------------------------------------------------------------
seq_length <- 30
sub_rate <- 1 / seq_length
input_tree <- TreeSim::sim.bd.taxa(n = 10,
numbsim = 1,
lambda = 1,
mu = 0.1,
complete = TRUE)[[1]]
normal_alignment <- sim_normal(input_tree,
l = seq_length,
rate = sub_rate)
plot_phyDat(normal_alignment$alignment)
## ----sim linkedunlinked-------------------------------------------------------
unlinked_alignment <- sim_unlinked(input_tree,
rate1 = sub_rate,
rate2 = sub_rate,
l = seq_length,
node_time = 0.5)
plot_phyDat(unlinked_alignment$alignment)
linked_alignment <- sim_linked(input_tree,
rate = sub_rate,
node_mut_rate_double = sub_rate * sub_rate,
node_time = 0.5,
l = seq_length)
plot_phyDat(linked_alignment$alignment)
## ----sim explicit-------------------------------------------------------------
unlinked_explicit <- sim_unlinked_explicit(input_tree,
rate1 = sub_rate,
rate2 = sub_rate,
l = seq_length,
node_time = 0.5)
plot_phyDat(unlinked_explicit$alignment)
normal_explicit <- sim_normal_explicit(input_tree,
l = seq_length,
rate = sub_rate)
plot_phyDat(normal_explicit$alignment)
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